# HG changeset patch
# User charles_s_test
# Date 1511913300 18000
# Node ID b04931a9fe7170fbc03a30f7d863d451541b4532
# Parent  3d6680af0bec4f080221967853899094792be438
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

diff -r 3d6680af0bec -r b04931a9fe71 seqsero.xml
--- a/seqsero.xml	Mon Nov 27 16:30:27 2017 -0500
+++ b/seqsero.xml	Tue Nov 28 18:55:00 2017 -0500
@@ -19,7 +19,7 @@
         </command> -->
             <command >
      
-                $__tool_directory__/run_seqsero.py $input1 $__tool_directory__/
+                python $__tool_directory__/run_seqsero.py $input1 $__tool_directory__/
                 
         </command> 
         <inputs>
diff -r 3d6680af0bec -r b04931a9fe71 seqsero.xml.2
--- a/seqsero.xml.2	Mon Nov 27 16:30:27 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<bookstore xmlns:xlink="http://www.w3.org/1999/xlink">
-
-<tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
-        <requirement type="package" version="1.69">biopython</requirement>
-        <requirement type="package" >samtools</requirement>
-        <description>Salmonella Serotype Prediction from Paired-End Reads</description>
-        <command interpreter="python2.7">
-                run_seqsero_batch_galaxy.py $input1 <!--$input2-->
-                <!--test_bioblend.py $input1 $input2-->
-        </command>
-        <inputs>
-                <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
-                <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
-        </inputs>
-        <outputs>
-                <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
-                <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
-        </outputs>
-        <help>
-              <!--This tool predicts Salmonella serotypes from shotgun WGS data.-->
-               .._htmlFile: "/nfs/sw/apps/galaxy/static/toolpages/seqsero/seqsero.html"
-        </help>
-        <citations>
-          <citation type="bibtex"> 
-          @Article{pmid25762776,
-               Author="Zhang, S.  and Yin, Y.  and Jones, M. B.  and Zhang, Z.  and Deatherage Kaiser, B. L.  and Dinsmore, B. A.  and Fitzgerald, C.  and Fields, P. I.  and Deng, X. ",
-                  Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
-                  Journal="J. Clin. Microbiol.",
-                  Year="2015",
-                  Volume="53",
-                  Number="5",
-                  Pages="1685--1692",
-                  Month="May"
-          }
-          </citation>
-        </citations>
-        <stdio>
-                <exit_code range="0:" level="warning"/>
-                <regex match="Error:"/>
-        </stdio>
-</tool>
diff -r 3d6680af0bec -r b04931a9fe71 seqsero.xml.2b
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqsero.xml.2b	Tue Nov 28 18:55:00 2017 -0500
@@ -0,0 +1,41 @@
+<bookstore xmlns:xlink="http://www.w3.org/1999/xlink">
+
+<tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
+        <requirement type="package" version="1.69">biopython</requirement>
+        <requirement type="package" >samtools</requirement>
+        <description>Salmonella Serotype Prediction from Paired-End Reads</description>
+        <command interpreter="python2.7">
+                run_seqsero_batch_galaxy.py $input1 <!--$input2-->
+                <!--test_bioblend.py $input1 $input2-->
+        </command>
+        <inputs>
+                <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
+                <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
+        </inputs>
+        <outputs>
+                <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
+                <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
+        </outputs>
+        <help>
+              <!--This tool predicts Salmonella serotypes from shotgun WGS data.-->
+               .._htmlFile: "/nfs/sw/apps/galaxy/static/toolpages/seqsero/seqsero.html"
+        </help>
+        <citations>
+          <citation type="bibtex"> 
+          @Article{pmid25762776,
+               Author="Zhang, S.  and Yin, Y.  and Jones, M. B.  and Zhang, Z.  and Deatherage Kaiser, B. L.  and Dinsmore, B. A.  and Fitzgerald, C.  and Fields, P. I.  and Deng, X. ",
+                  Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
+                  Journal="J. Clin. Microbiol.",
+                  Year="2015",
+                  Volume="53",
+                  Number="5",
+                  Pages="1685--1692",
+                  Month="May"
+          }
+          </citation>
+        </citations>
+        <stdio>
+                <exit_code range="0:" level="warning"/>
+                <regex match="Error:"/>
+        </stdio>
+</tool>
diff -r 3d6680af0bec -r b04931a9fe71 test.txt
--- a/test.txt	Mon Nov 27 16:30:27 2017 -0500
+++ b/test.txt	Tue Nov 28 18:55:00 2017 -0500
@@ -19,4 +19,4 @@
 
 
 None
-Mon Nov 27 16:25:00 2017
\ No newline at end of file
+Mon Nov 27 16:46:44 2017
\ No newline at end of file